Nintendo
Super Mario Brothers
Bowser: Defeated in many various ways
Bowser Jr.: Defeated in many various ways
The Koopalings: Defeated in many various ways
Donkey Kong from the video game of the same name: Falls off the stage
Donkey Kong
King K. Roll: Defeated in many various ways
The Legend of Zelda
Ganondorf: Defeated in many various ways
Pokemon
Mewtwo: Defeated in many various ways
Kirby
King DeDeDe: Defeated in many various ways
Marx from Kirby Ultra Super Star: Slain by Kirby and then explodes
Metroid
Ridley: Defeated in many various ways
Dark Samus from Metroid Prime 3: Corruption: Her monster form was destroyed and then she explodes.
Kid Icarus
Hades from Kid Icarus: Uprising: Defeated in many various ways
Sega
Sonic the Hedgehog
Dr. Ivo "Eggman" Robotnik from Sonic the Hedgehog: Defeated in many various ways
Capcom
Mega Man
Dr Wily: Defeated in many various ways
Sony Interactive Entertainment
Dr Neo Cortex from Crash Bandicoot: Defeated in many various ways
Square Enix
Final Fanatsy
Sepiroth from Final Fanatsy VII:
Dragon Quest
Kingdom Hearts
Assem, Seeker of Darkness:
Activision
Blizzard
Bandai Namco Entertainment
Electronic Arts
Epic Games
Konami
Marvelous
NCSoft
NetEase
Nexon
Nippon Ichi
SNK
Take-Two Interactive
Tencent
Ubisoft
Xbox Game Studios
Others Games
Indie Games
Monika from Doki Doki Literature Club: Gets deleted from existence